Background: Pilonidal sinus is a common disease in the sacrococcygeal region. Although many treatments have been described in recent years, the recurrence of each method remains high. Surgeons did not reach a consensus on the preferred approach for pilonidal sinus. We carried out a meta-analysis of controlled clinical trials comparing the outcomes of endoscopic treatment versus conventional treatment for pilonidal sinus disease in this study.Methods: We performed a systematic literature search, and we used electronic databases such as PubMed/Medline, Embase, and the Cochrane library to search for the relevant literature comparing endoscopic management to other conventional treatments for pilonidal sinus disease. The primary outcome parameters were operative time, recurrence, postoperative complications and pain, and total healing time.Results: Six studies were included in the review. Endoscopic pilonidal sinus treatment had a lower overall complication rate than the conventional surgery group (risk ratio = 0.33 [0.19-0.58], P = .0001) and lower pain score with a weighted mean difference of −2.44 (95% confidence interval: (−3.96) to (−0.92), I 2 = 99%, P = .002). There was no significant difference in recurrence (risk ratio = 0.75, 95% confidence interval [0.30-1.90],P = .55). Compared to the excision followed by the primary closure technique, the operation time, time to complete wound healing, and satisfaction were similar.Conclusions: Endoscopic pilonidal sinus treatment is a unique and potential method of sacrococcygeal pilonidal disease treatment. The foremost benefits of this technique are mild postoperative pain, lower complications rate, and return to routine for a shorter time. However, due to the limited number of articles, we need to conduct more rigorous large-sample prospective randomized controlled trials to clarify the efficiency of endoscopic treatment for pilonidal cysts.Abbreviations: CI = confidence interval, EHSI = en-bloc excision and healing by secondary intention, EPC = excision and primary closure, EPSiT = endoscopic pilonidal sinus treatment, ERAS = enhanced recovery after surgery, NA = Not available, PSD = pilonidal sinus disease, RCT = randomized controlled trial, RR = risk ratio.